The posre itp file represents one lipid molecule and the p2.itp file
represents all water molecules.
I have a p1.itp file that represents one water molecule but this also
brought up the :
cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
-I/usr/local/share/gromacs/top -DPOSRES dopc.top > grompptByAm1'
message.
TOP FILE:
#include "/home/tripos/lipid/ffgmx2_lipid.itp"
#include "/home/tripos/lipid/DOPCHT.itp"
#include "/usr/local/share/gromacs/top/spc.itp"
[ system ]
; name
DOPC in water
#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water
;#include "/home/tripos/lipid/dopc/minidopc/p2.itp" in water
#endif
[ molecules ]
; name number
DOPC 18
SOL 1463
Quoting Yang Ye <[EMAIL PROTECTED]>:
You shall append those three lines just under the definition of the
lipid molecule. You may paste your top file for us to comment.
Yang Ye
Farid Sa'adedin wrote:
Dear Users,
I have been trying to equilibrate a bilayer. I have been able to
restrain a bilayer in its own system using
#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp"
#endif
in the topology file
define = -DPOSRES
in the steep, nvt and npt mdp files.
The problem occurs when I add water to the system and for some
reason when I just want to restrain the
the bilayer GROMACS doesn't recognise the posre.itp file even though
it becomes in the top.
#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water
#endif
This is the line I get when I run grompp:
cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
-I/usr/local/share/gromacs/top -DPOSRES dopc.top > grompptByAm1'
So as a result it doesn't restrain the lipids in the simulation.
If anyone has any ideas on how to just restrain a lipids with water
in the system I would greatly appreciate them.
Yours sincerely,
Farid Sa'adedin--
Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Summerhall
Edinburgh EH9 1QH
SCOTLAND
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